[R-sig-phylo] ape::muscle doesn't work with Muscle5

Hello, ape::muscle() works well with MUSCLE 3.8.31 from , but not with v. 5.1 (released recently). I run it as 'ape::muscle(x=gunnera.dna, exec="muscle", quiet=FALSE, original.ordering=TRUE)' and I get

Re: [R-sig-phylo] ape: error in pcoa

Many thanks Emmanuel for the detailed instructions and sorry for the messed up formatting. Best Juan El 24/04/2021 a las 9:03, Emmanuel Paradis escribió: > Hi Juan, > > There is a bug in pcoa() when only one axis is selected by the function. You > can fix it by editing the function with

Re: [R-sig-phylo] ape: error in pcoa

Hi Juan, There is a bug in pcoa() when only one axis is selected by the function. You can fix it by editing the function with fix(pcoa) and modify line 38 (or close depending on how the editor arranges the lines of code): vectors <- sweep(D.eig$vectors[, 1:k], 2, sqrt(eig[1:k]), FUN = "*")

[R-sig-phylo] ape: error in pcoa

Hellow, I am running a set of simulations with distance matrices used as input to pcoa (package ape). In one instance the matrix (DH) is H18 H20 H21 H18 0.000 0.3127452190 0.3127452190 H20 0.3127452 0.00 0.0001625185 H21 0.3127452 0.0001625185 0.00 when I run pcoa I get

Re: [R-sig-phylo] ape package in R

Hi, Actually, Ranjita can use the number of gene copies if it is reasonable to assume that these numbers evolve among samples, maybe a stepwise model with transitions: n -> n + 1 n -> n - 1 In that case, a simple approach is to calculate the Euclidean distances among samples and do an NJ or

Re: [R-sig-phylo] ape package in R

If you want to use ape for making a phylogenetic tree, I think you need the actual sequences of the genes, and not only the copy numbers El sáb., 19 sept. 2020 a las 21:40, Ranjita Thapa () escribió: > Hi, > > I want to construct a phylogenetic tree with ape package. I have a csv > file with

[R-sig-phylo] ape package in R

Hi, I want to construct a phylogenetic tree with ape package. I have a csv file with gene ids and copy number for each gene across different samples. I want to construct phylogenetic tree. I am wondering how could I convert the csv file to input file for ape. Could you please suggest me how

Re: [R-sig-phylo] ape chronos function returning pLL of -1E100

S Denton Sent: Wednesday, December 12, 2018 1:20:20 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] ape chronos function returning pLL of -1E100 I'm trying to use chronos (ape version 5.2) to scale a tree of ~800 tips, with branch lengths derived from a RAxML analysis. I'm using 4

Re: [R-sig-phylo] ape chronos function returning pLL of -1E100

nodes with conflicting ages, and R does not give errors about the formatting of the calibration table. ~John From: R-sig-phylo on behalf of John S Denton Sent: Wednesday, December 12, 2018 1:20:20 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] ape

[R-sig-phylo] ape chronos function returning pLL of -1E100

I'm trying to use chronos (ape version 5.2) to scale a tree of ~800 tips, with branch lengths derived from a RAxML analysis. I'm using 4 outgroup calibrations. When I run the analysis using t.og <- chronos(tree, lambda = 1, model = "relaxed", quiet = FALSE, calibration = dd.out) I

Re: [R-sig-phylo] ape-package: unknown states in ace analyses?

Paradis Envoy� : vendredi, 22 juin 2018 15:45:05 � : Th�o L�ger; r-sig-phylo@r-project.org Objet : Re: [R-sig-phylo] ape-package: unknown states in ace analyses? Two more comments: 1/ The first insertion in the code of ace() below is not needed if the user replaces "?" (or any coding fo

Re: [R-sig-phylo] ape-package: unknown states in ace analyses?

This is so cool. Thanks Liam! J > On Jun 21, 2018, at 8:22 PM, Liam J. Revell wrote: > > Dear Theo. > > This can be done with the function rerootingMethod as described here > http://blog.phytools.org/2013/04/estimating-ancestral-states-when.html, > although it is *very* important to note

Re: [R-sig-phylo] ape-package: unknown states in ace analyses?

Two more comments: 1/ The first insertion in the code of ace() below is not needed if the user replaces "?" (or any coding for unknown/uncertain state) with NA -- which seems reasonable to do. 2/ This approach of taking uncertainty into account in likelihood ancestral state reconstruction

Re: [R-sig-phylo] ape-package: unknown states in ace analyses?

Hi Théo, It is possible to modify the code of ace() to take uncertain character states into account. If you edit the code with fix(ace), after these four lines: if (method != "ML") stop("only ML estimation is possible for discrete characters.") if (any(phy$edge.length <= 0))

[R-sig-phylo] ape-package: unknown states in ace analyses?

Hello, I am working on the phylogeny of a subfamily of moths and I use ace from the ape-package to reconstruct the ancestral state of a bunch of morphological characters. I encountered a problem with the few unknown states I have on my matrix (coded "?", either because material for

[R-sig-phylo] Ape

Hello, I use R on a mac (sierra) I use « Iramuteq » working under R using page library My problème is to change the ape version to get back to older version (from 5 back to 3.5) I am not familiar with commands... could someone help me? If possible by giving the code lines i would have to put

Re: [R-sig-phylo] ape

Hi, You can find all released versions of ape as source packages on CRAN: https://cran.r-project.org/src/contrib/Archive/ape/ Best, Emmanuel Le 07/12/2017 à 11:19, pascal de Clarens a écrit : Hello, I am using Iramutec working togethr with R it needs to use ape 3.5 annd having installed

[R-sig-phylo] ape

Hello, I am using Iramutec working togethr with R it needs to use ape 3.5 annd having installed and updated the libraries, , the one currently installed (mac Sierre 10.13) is the version 5 I therefore need to delete the lates versin and install the 'old' 3.3 ape version I need help as I do not

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

Dears, I removed ape 4.1 and install 4.0 version and the problem with my tree is gone. I can extract clade even my tree having singletons. But the problem still occur in example tree, with new error message. With this tree: A_1,A_2,)A,(B1,B2,B3)B)C,D1))),(E1,E2)E)D),(F1)F)R; or

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

Dear Eliot, Thank you for your answer! My tree is ok, but to plot is needed to collapse singles, as you said. I use ape/phytools to manipulate my tree for date it after with phylocom. Then, all node is important, including single one. For this, collapse singletons do not work for me. For

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

Dear Klaus, Thank you for your answer and good news that ape/phangorn will load tree with singletons! Can I send the tree to your email? My problem with collapse.singles is, for instance, when I have only one genus/specie. I want the node name with genus and a tip name with species. When I

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

Your Newick string is badly formatted. See: plot(t1) Error in plot.phylo(t1) : there are single (non-splitting) nodes in your tree; you may need to use collapse.singles() On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo < mariojm...@gmail.com> wrote: > Dears, > > I'm using

[R-sig-phylo] ape package: improvement suggestion in color handling for mosaic in phydataplot?

Dear all, I am trying to use the phydataplot function in the ape package with the style mosaic. I am having difficulty getting the colors of the rectangles to be the color I desire in an automatic way. I have come to the conclusion that I can’t do and it would have to be an enhancement to the

Re: [R-sig-phylo] ape - corMartins

ds, Sérgio. - Mensagem original - > De: "Emmanuel Paradis" <emmanuel.para...@ird.fr> > Para: "Sergio Ferreira Cardoso" <sff.card...@campus.fct.unl.pt>, > "r-sig-phylo" <r-sig-phylo@r-project.org> > Enviadas: Terça-feira, 24 De Janei

Re: [R-sig-phylo] ape - corMartins

Hi Sérgio, It seems your results make good sense. alpha=0 is too far from the "optimum" value (i.e., the value that maximises the log-lik), so the optimisation fails to maximise the log-likelihood with respect to this parameter. It has been written in the literature that it is difficult to

[R-sig-phylo] ape - corMartins

Dear all, I tried to estimate a value for alpha parameter of corMartins (Ornstein-Uhlenbeck) but the output is a bit puzzling. I do as follows: >

Re: [R-sig-phylo] ape chronos error

Following Riana's query, it appeared that the tree she used had no branch lengths. chronos() now check for the presence of branch lengths and returns an explicit error message. Best, Emmanuel Le 16/12/2016 à 18:20, Emmanuel Paradis a écrit : Hi Riana, It's difficult to answer your

Re: [R-sig-phylo] ape chronos error

Hi Riana, It's difficult to answer your question. Can you send some sample data to reproduce this error? Best, Emmanuel Le 15/12/2016 à 22:58, Riana Rishad Minocher a écrit : Hi, I’m writing with an issue using the chronos function in ape: I have a rooted supertree of 186 taxa (genetic &

[R-sig-phylo] ape chronos error

Hi, I’m writing with an issue using the chronos function in ape: I have a rooted supertree of 186 taxa (genetic & linguistic data), and am trying to time-calibrate with a set of divergence dates (genetic & linguistic; available for about 1/3 of nodes). I’m using chronos and calling agemin

Re: [R-sig-phylo] ape functions to become generic

Thanks, Emmanuel. That answers my questions. Cheers, -Dave On Tue, Oct 4, 2016 at 4:03 AM, Emmanuel Paradis wrote: > Hi David, > > Le 03/10/2016 à 17:25, David Bapst a écrit : >> >> Hi Emmanuel (and list!), >> >> These changes are appreciated, and will make dealing

Re: [R-sig-phylo] ape functions to become generic

Hi David, Le 03/10/2016 à 17:25, David Bapst a écrit : Hi Emmanuel (and list!), These changes are appreciated, and will make dealing with multiPhylo objects much easier. I know I certainly have blocks of code where I need to 'carry' the multiPhylo class tag through every other line; it always

Re: [R-sig-phylo] ape functions to become generic

Hi Emmanuel (and list!), These changes are appreciated, and will make dealing with multiPhylo objects much easier. I know I certainly have blocks of code where I need to 'carry' the multiPhylo class tag through every other line; it always been a bit of a chore. However, two questions from the

[R-sig-phylo] ape functions to become generic

Dear all, We are planning to introduce a substantial change in ape: several functions operating on "phylo" objects will be made generic with methods for "phylo" and "multiPhylo" objects. The motivation is to make things simpler when working with lists of trees. For instance, for a list of

[R-sig-phylo] ape - nj, mvr questions

I am currently using ape package to construct genetic trees for my research, and i am using nj() and mvr() functions 1.i was wondering if there is a way, to create the genetic tree, assuming that one of the samples, might be an inner node of the tree, and not necessarily a leaf of the tree (for

Re: [R-sig-phylo] ape: chronos

Hi Daniel, Thank you for your report. It's not very clear how or why the penalized likelihood becomes NA (maybe a log of a negative number is calculated somewhere). chronos() is still under progress and I take good note of your fix. Best, Emmanuel Le 05/09/2016 à 10:27, Daniel Lang a

[R-sig-phylo] ape: chronos

Hi, I hope I did not overlook ape's bug tracker - which would be the most appropriate place to post the following: I ran into this error while dating a tree using apes' chronos function (discrete model): Error in if (new.ploglik - current.ploglik > 1e-06 && i <= dual.iter.max) { : missing

Re: [R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument'

Emmanuel Paradis writes: > > Hi Matt, > > This is because this accession number does not point to the sequence. > For this particular one, you could use: > > seq1 <- read.GenBank("U00096.3") > > Best, > > Emmanuel > > Le 27/02/2014 01:35, Matt Curcio a écrit : > >

[R-sig-phylo] Ape Plot issues

Anyone having issues with plot functions? Specifically with Plot commands, myself and a colleague could not get the command 'plot(phy, show.node.label=TRUE)' to work. Anyone else having similar problems? Many thanks, Jessica -- Jessica E. Light Assistant Professor and Curator of Mammals

Re: [R-sig-phylo] Ape Plot issues

Hi Jessica. Are you sure your tree has node labels? If it does not, then none will be plotted. (This is unlike the function nodelabels which, if not supplied with any arguments, will just plot the node indices at the nodes of the plotted tree.) E.g., library(ape)

[R-sig-phylo] ape: read.nexus/write.nexus and recursive tree name expansion

Hi, Ape seems to have a problem with parsing tree names in nexus files. This can cause problems when using the .nex with other programs. library(ape) packageVersion(ape) [1] '3.1.4' t - c(read.tree(text=((a:0.1,b:0.2):0.3,c:0.45);), read.tree(text=((a:0.1,b:0.2):0.3,c:0.55);)) names(t) -

Re: [R-sig-phylo] ape: read.nexus/write.nexus and recursive tree name expansion

Something like the patch below might be appropriate. -Graham --- read.nexus.R.bak2014-10-20 14:56:57.0 +1030 +++ read.nexus.R2014-10-20 15:11:26.0 +1030 @@ -183,7 +183,7 @@ Ntree - length(STRING) # update Ntree ## get the tree names: nms.trees - sub( *=

Re: [R-sig-phylo] Ape package.

You need put the path of the directory with this simbol / and not this \, so the correct path is F:*/*tetrapods_tree.txt. Cheers! On Sun, Apr 20, 2014 at 5:17 PM, Alexey Fomin lesh...@rambler.ru wrote: Hi! Whether someone work with ape package? I have long tree (see attached, it is in

Re: [R-sig-phylo] Ape package.

The tree file is not proper formatted, it is missing a ; in the end. Regards, Klaus On Sun, Apr 20, 2014 at 10:17 PM, Alexey Fomin lesh...@rambler.ru wrote: Hi! Whether someone work with ape package? I have long tree (see attached, it is in newick format, it is ultra metric, it is from

[R-sig-phylo] ape package.

Whether anybody help? I can non start the ape package. when I do library(ape) it give: Error in library(ape) : there is no package called 'ape' (I use R-3.0.3-win) ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org

[R-sig-phylo] ape cophyloplot strange horizontal lines

Hi,Im plotting a cophylogeny using cophyloplot {ape}.Im running;cophyloplot(bugs_tree,sponge_tree,assoc = con,type="cladogram", space=200, gap=0,show.tip.label=F, use.edge.length=F)where bugs_tree and sponge_tree are the two phylogenies and con is the association between the tips of the

Re: [R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument'

Hi Matt, This is because this accession number does not point to the sequence. For this particular one, you could use: seq1 - read.GenBank(U00096.3) Best, Emmanuel Le 27/02/2014 01:35, Matt Curcio a écrit : Greetings all,, I received this error while using R version 2.15.1 and ape 3.0.11.

[R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument'

Greetings all,, I received this error while using R version 2.15.1 and ape 3.0.11. Error in FI[i]:LA[i] : NA/NaN argument I have tried several approaches: ref = NC_000913.3 seq1 = read.GenBank(ref) Error in FI[i]:LA[i] : NA/NaN argument ref = read.csv(file=test2.csv, head=T) ref = str(ref) #

[R-sig-phylo] APE error message

Hello all I'm new with APE. I'm trying to open a NEXUS tree with 109 sp and with many polytomies and I received the following error message: Error en trees[[i]] : subíndice fuera de los límites Anyone know what that the error means? Ape has a maximum number of species? thanks! Fernando --

Re: [R-sig-phylo] APE error message

Are you trying to load a single tree or multiple trees in a single Nexus file? What function are you trying to use to load the tree(s)? On Mon, Sep 16, 2013 at 5:46 PM, BIGANZOLI FERNANDO bigan...@agro.uba.arwrote: Hello all I'm new with APE. I'm trying to open a NEXUS tree with 109 sp and

Re: [R-sig-phylo] ape and pvclust

to take advantage of the flexibility of plot.phylo. This might be your solution too. Viren -Original Message- From: Gilles Benjamin Leduc [mailto:g...@hi.is] Sent: Saturday, December 01, 2012 5:20 PM To: Viky Koralkova Cc: Amin, Viren; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo

[R-sig-phylo] ape and pvclust

Mathias, I am also currently trying on plotting au/bp values from pvclust to tree plot from ape package. Were you able to figure this out? If you did, I would really appreciate if you can provide me tips. Thanks Viren [[alternative HTML version deleted]]

[R-sig-phylo] Ape: dist.dna, P-distance calculation

Hi all, I am calculating P-distances using dist.dna (pdistance - dist.dna(convertdata, model = raw). WHen I did this, I got abnormally high p-distances in the .9 region. I then calculated the p distance using Paup and I got more normal values. Ultimately, I would like to use R to calculate

Re: [R-sig-phylo] Ape: dist.dna, P-distance calculation

Subject: [R-sig-phylo] Ape: dist.dna, P-distance calculation Hi all, I am calculating P-distances using dist.dna (pdistance - dist.dna(convertdata, model = raw). WHen I did this, I got abnormally high p-distances in the .9 region. I then calculated the p distance using Paup and I got more normal values

Re: [R-sig-phylo] ape and pvclust

Sender: r-sig-phylo-boun...@r-project.org Date: Sat, 19 Nov 2011 10:26:02 To: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] ape and pvclust Hi Mathias, a fast way to see/check the order of nodes in the tree (before assigning any values to the nodes) is: plot(mytree) nodelabels

[R-sig-phylo] ape and pvclust

Hi, I wonder if it's possible to plot the au and bp values computed by pvclust on the nodes of an pyhlo tree of the ape package. It should look like here: http://treethinkers.blogspot.com/2008/10/labeling-trees-posterior-probability.html I tried to transfer the computed values put they are not

Re: [R-sig-phylo] ape and pvclust

Hi Mathias, a fast way to see/check the order of nodes in the tree (before assigning any values to the nodes) is: plot(mytree) nodelabels() The labels you need to show will then have to be a vector with its elements in the order of the numbering of nodes you see in the tree. Normally nodes

[R-sig-phylo] APE incomplete distances

Dear all, As part of my Google Summer of Code project I have extended APE with some methods for reconstructing phylogenetic trees from incomplete distances. They are NJ*, bio-NJ* ([1]) and the triangles method [2]. Since they have not yet been included into the official release of APE you can

Re: [R-sig-phylo] ape processing time

On 11-06-13 12:02 PM, alfredo tello wrote: Hi Folks, Can anyone tell me how to roughly calculate the processing time required to compute a phylogenetic matrix (K80) with ape given a certain hardware? I just want to have a rough idea before pressing Go Try running a few tiny- to

Re: [R-sig-phylo] ape Crashes latest version does not install

Here is another error message. They appear when I run boot.phylo. I tried using set.seed to see if that worked, but it didn't. boot.eryth-boot.phylo(eryth.bionj,erythSeq,function(x){bionj(dist.dna(x, model = K80))}) *** caught segfault *** address 0x38, cause 'memory not mapped' Traceback:

Re: [R-sig-phylo] ape Crashes latest version does not install

2011 13:25:18 To: Carl Boettigercboet...@gmail.com Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] ape Crashes latest version does not install Here is another error message. They appear when I run boot.phylo. I tried using set.seed to see if that worked, but it didn't. boot.eryth

Re: [R-sig-phylo] ape Crashes latest version does not install

...@gmail.com Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] ape Crashes latest version does not install Here is another error message. They appear when I run boot.phylo. I tried using set.seed to see if that worked, but it didn't. boot.eryth-boot.phylo(eryth.bionj,erythSeq,function(x

Re: [R-sig-phylo] ape Crashes latest version does not install

-project.org; Carl Boettigercboet...@gmail.com; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] ape Crashes latest version does not install I have rerun the analysis using nj instead of bionj and no longer get problems. Perhaps my distances are too big (¿?¿?). Any comments would be appreciated. Best

[R-sig-phylo] ape Crashes latest version does not install

Hi Folks, I've been using ape for a few weeks now and it crashes probably once a day. If I close R, re-open it and re-run the ape function it normally works fine. I have tried to install the latest version of ape, which might solve the problem, but get an error when installing it. Perhaps the

Re: [R-sig-phylo] ape-package/ possibility to get the transformed residuals (phylogentic corrected residuals)?

Actually, the function residuals.gls calculates 3 different types of residuals: response or raw residuals, pearson or standardized residuals, and normalized residuals. For diagnostic purposes, you probably want the normalized residuals. The default is the response residuals (although the

Re: [R-sig-phylo] APE: zoom with polytomies

Thanks Christoph! That was the problem!! I could not find the phyloch in the CRAN package repository, though. But your solution number 1 did the trick. F On Feb 18, 2010, at 2:41 AM, Christoph Heibl wrote: A question for ape/adephylo users/developers: I am trying to use the function

Re: [R-sig-phylo] ape matrix manipulation

Hi Gustavo, Hava a look at: ?`%in%` Given a matrix 's' of class DNAbin and a tree 'tr' of class phylo, you simply do: s - s[-(rownames(s) %in% tr$tip.label), ] Of course this requires matching taxon names in s and tr... HTH Christoph

Re: [R-sig-phylo] ape matrix manipulation

Hi Gustavo, I wrote a function to randomly prune one of the two alleles for each species in an alignment and tree list (say from MrBayes). I create a list of names that I want to drop, and I prune them out of the dataset and treelist (so I have a matching dataset for each treefile). It's not

Re: [R-sig-phylo] ape matrix manipulation

Hi Christoph Gustavo, Quoting Christoph Heibl christoph.he...@gmx.net: Hi Gustavo, Hava a look at: ?`%in%` Given a matrix 's' of class DNAbin and a tree 'tr' of class phylo, you simply do: s - s[-(rownames(s) %in% tr$tip.label), ] Yes but replace '-' with '!': s - s[!(rownames(s) %in%

[R-sig-phylo] ape matrix manipulation

Hello, I am working with a more less a big phylogeny (over 100 taxa). I had used drop.tips to analyze some clades independently and produce sub-trees. My question is: how can I use the information in the modified trees to drop the same taxa in the original DNA matrix? I have been doing this